Compose a 250 words assignment on chemistry. Needs to be plagiarism free! Access to Higher Education Unit Biochemistry LO3 (Enzymes), Criteria 3 to 3.4 To achieve level 3, answer all questions correct

Compose a 250 words assignment on chemistry. Needs to be plagiarism free! Access to Higher Education Unit Biochemistry LO3 (Enzymes), Criteria 3 to 3.4 To achieve level 3, answer all questions correctly. Level 3(Assessment Criterion 3.1)

Q1Almost all chemical reactions in living organisms depend on enzymes.

a) Give a brief definition of an enzyme.

An enzyme is an organic molecule that acts as a catalyst for many biological reactions. Most are protein in nature but some are RNA in nature. They are highly specific and sensitive (Klaus Buchholz, 2012) to the substrates and conditions in which they function.

b)Explain two similarities and two differences between the way an enzyme works on one hand and an inorganic catalyst on the other.

Similarities. Both an enzyme and an inorganic catalyst work by reducing the activation energy (Gibbs energy) (Thermodynamics, 2013)required to facilitate a reaction.

Both an enzyme and inorganic catalyst are also sensitive to conditions in a reaction. For example, most enzymes are sensitive to pH and temperature. The same is true for some catalysts such as manganese salts that are pH sensitive and heat sensitive, requiring controlled conditions to work. (Klaus Buchholz, 2012)

Both enzymes and catalysts also have positive and negative catalysis. Enzymes are either activators or inhibitors, while the inorganic are either negative or positive catalysts.

Differences. Enzymes are organic, containing protein sub-groups. As such they are high molecular weight compounds. Inorganic catalysts are often low molecular weight. Inorganic catalysts are more resilient to changes in temperatures. An example is Pt/Rh catalysts used at high temperatures. This is compared to organic catalysts that denature past a certain temperature (mostly 40 degrees Celsius).

Enzymes are also manufactured by biological systems, and as such most are highly specific to the reactions and substrates they require for such. Inorganic catalysts are sometimes ambiguous. They catalyse numerous reactions as long as the conditions are right. For example Platinum, Pt is a catalyst for a wide range of industrial processes.

Enzymes are also several times faster in their catalyzing of reactions compared to inorganic catalysts

Level 3 (Assessment Criterion 3.2)

Q2There are two main concepts regarding the mechanisms of enzyme specificity.

a) Name and explain one of these theories.

Lock and key model- this model was proposed by Emil fischer. It states that an enzyme is like a lock, while a substrate is like a key. As such, an enzyme can only be bound by a specific type of substrate (Spencer Seager, 2013) and this means that for any given enzyme, the substrate has to be specific or highly similar to the substrate for the reaction to occur. This model/ theory shows the enzyme as conformationally rigid and able to only act on substrates that are an exact fit. (Timberlake, 2014)

b) Name and explain the other theory of enzyme specificity.

Koshland’s induced fit theory- this theory states that an enzyme is not a rigid structure. As a substrate binds, it leads to conformational change that enhances the enzymes ability to carry out its catalytic function. In some cases the enzymes active site is remoulded completely and the charge of the enzyme also modified as it binds to its substrate. (Spencer Seager, 2013) After catalysis has been carried out, the enzyme resumes its original shape.

(Timberlake, 2014)

Level 3 (Assessment Criterion 3.3)

Q3 You are an investigator and your research group has just isolated two novel enzymes A and B that are both secreted into the small intestine of the domestic pig Sus scrofa. You would like to have these enzymes characterised. Therefore you have asked your project student Tamsyn to determine the pH optimum of enzyme A. Likewise. you have also asked your other project student Tom to determine the pH optimum of enzyme B.

a) At the next weekly lab meeting, Tamsyn presents her results from a single set of measurements on enzyme A:

pH

1

2

3

4

5

6

7

8

9

10

11

12

13

Activity

3

1

0

2

1

43

78

82

65

5

1

3

0

Several lab members believe that Tamsyn’s data look promising. They suggest that she should repeat the experiment at least two more times, but leave her experimental conditions the same. Do you agree that the data look promising? Explain why or why not (a graph might be useful).

I do agree that the data is promising. Most enzymes work at an optimum pH. As shown by the graph, this enzyme works best at pH8. The small intestine pH is about 7.4

b) At the same meeting, Tom also presents a single set of measurements on enzyme B:

pH

1

2

3

4

5

6

7

8

9

10

11

12

13

Activity

2

10

5

3

1

5

6

7

6

3

6

2

4

Tom claims that his data indicate a pH optimum at pH 2. Some lab members are skeptical. What do you think? Explain.

I would be sceptical as the pH 2 is quite low for the small intestine. Furthermore, the fact that the optimum activity seems to be spread on different peaks is a false representation of an enzyme. Enzymes are known to be pH specific

c) Some lab members suggest that Tom should try to get higher activity readings. Tom proposes to double the substrate concentration next time, because that would automatically double the speed of the reaction. Is this correct? Explain.

This is not correct. The speed of an enzyme, Vmax is affected by factors such as temperature and pH that have to be optimum. Adding the substrate would only serve to reach enzyme saturation faster. The addition of substrate is thus not correct.

d) The next day, Tamsyn notices that Tom has the water bath that he does his enzyme incubations in set to 550C. She claims that this temperature is not appropriate and suggests a different temperature for Tom’s experiment. Explain why Tom might have chosen this temperature, why Tamsyn has a point, and what temperature you would suggest to Tom.

I would suggest a lower temperature between 35 and 38 degrees Celsius (Biologists, 2014). Any higher temperature risks denaturing the enzyme while lower temperatures lower activity. Tamsyn thus has a point in asking him to change the temperature. Tom may have chosen this temperature in an attempt to increase enzyme activity.

Level 3 (Assessment Criterion 3.4)

Q 4 Enzymes have many important functions in living cells.

a) What enzyme produces ATP in mitochondria? Where is it found, and how does it produce ATP?

ATP synthase. It has two parts -F0 and F1

The F0 portion is found inside the inner mitochondrial membrane while the F1 is found in the mitochondrial matrix. (Weber, 2014)

Production of ATP is facilitated by the enzyme above. The process is known as chemiosmosis. It is powered by a proton gradient across the inner mitochondrial membrane. The movement of electrons through the respiratory chain facilitates the pumping of protons from the matrix to the cytosolic side of the inner mitochondrial membrane. The proton concentration then becomes lower in the matrix, and an electrical field is generated. This gradient powers the ADP +Pi reaction that forms ATP as the protons escape. This is a form of reaction that harnesses entropic energy.

(medics, 2012)

b) Name two enzymes that can synthesise nucleic acids. Briefly outline the reactions that they catalyse.

DNA polymerase- These are a family of enzymes that work in pairs, one on each DNA strand. DNA polymerases are responsible for adding free nucleotides to the 3 end of a newly forming DNA strand as the enzyme requires a free 3 OH group for initiation of the process. They exist in all organisms (prokaryotes and eukaryotes) in different forms. Prokaryotes-Pol I-V, Eukaryotes- for example Polymerases β, λ, σ and μ found mainly in vertebrates.

Primase- responsible for synthesizing the RNA molecules that form the first two bases during DNA replication. In actual sense, this enzyme is a polymerase that creates the primer end of the DNA. &nbsp.The Primase enzyme is activated by&nbsp.DNA helicase.&nbsp.It synthesizes a short RNA primer approximately eleven&nbsp.nucleotides long that provide the beginning for the rest of the DNA to be assembled. DNAg is an example of a primase found in bacteria.

Bibliography 1 (Enzymes)

A, N. (2014).&nbsp.Biochemistry for medics. [online] Biochemistry for medics. Available at: http://www.namrata.co/electron-transport-chain-an-over-view-solution-to-problem-based-on-etc/. Last accessed 4/05/2014. [Accessed 10 May. 2014].

Biologists, C. (2014).&nbsp.Chemistry for Biologists: Enzymes. [online] Rsc.org. Available at: http://www.rsc.org/Education/Teachers/Resources/cfb/enzymes.htm [Accessed 10 May. 2014].

Joachim Weber. (2014).&nbsp.ATP synthase.&nbsp.Available: http://www.depts.ttu.edu/chemistry/Faculty/weber/. Last accessed 4/05/2014.

Karen C. Timberlake (2011).&nbsp.Introduction to Chemistry: General, Organic, and Biological. New York: Pearson education. 744

Klaus Buchholz, Volker Kasche, Uwe Theo Bornscheuer (2012).Biocatalysts and Enzyme Technology. newyork: John Wiley & Sons. 626.

Spencer Seager, Michael Slabaugh (2013).&nbsp.Organic and Biochemistry for Today. New York: Cengage learning. 544.

Thermodynamics. (2013).&nbsp.Thermodynamics.&nbsp.Available: https://www.chem.tamu.edu/class/majors/tutorialnotefiles/gibbs.htm. Last accessed 4/05/2014

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Unit Title: Biochemistry

LO4 (Lipids), Criteria 4.1 to 4.3

To achieve level 3, answer all questions correctly.

Level 3 (Assessment Criterion 4.1)

Q1What are lipids?

These are naturally occurring polymers of fatty acids and glycerol, prenols, sugars or other compounds (AOCK, 2014). They include the common fats and waxes

(J.E. Vance, 2008)

Level 3 (Assessment Criterion 4.2)

Q2Draw the structural formula

a) of glycerol

It is basically propan-1,2,3- triol

(J.E. Vance, 2008)

b) of a fatty acid

Butyric acid (J.E. Vance, 2008)

c) of a triacylglycerol

Basic structure of a triacylglycerol (J.E. Vance, 2008)

Tripalmitin

(David W. Ball, 2013)Q3What is the biological importance of triacylglycerols?

Triacyl glycerols have many uses.

They contribute to the formation of cell membranes

They act as thermal insulation

They are a source of energy and metabolic water in organisms like camels

They act as biological shock absorbers in joints (Bender, 2014).

Level 3 (Assessment Criterion 4.3)

Q4 Draw the structural formula of a phospholipid with

One saturated and one monounsaturated fatty acid.

(J.E. Vance, 2008) (Vance, 2008)

(Vance, 2008)

Q5 Briefly describe the major role of phospholipids in living organisms.

They are the major component of the lipid bi-membranes (Education, 2014). They form hydrophobic and hydrophilic parts that facilitate the protection of the internal cell environment by forming envelopes.

Bibliography 2 (lipids)

AOCK, (2014).&nbsp.Lipids, fatty acids, structure, composition, biochemistry and function. [online] Lipidlibrary.aocs.org. Available at: http://lipidlibrary.aocs.org/Lipids/whatlip/index.htm [Accessed 10 May. 2014].

Bender, H. (2014).&nbsp.Functions of Triglycerides. [online] Dl.clackamas.edu. Available at: http://dl.clackamas.edu/ch106-06/function.htm [Accessed 10 May. 2014].

David W. Ball, John W hill, Rhonda J. Scott (2011).&nbsp.The Basics of General,organic,and Biological Chemistry. New York: Elsevier. 624.

Education, E. (2014).&nbsp.Phosphoglycerides. [online] Elmhurst.edu. Available at: http://www.elmhurst.edu/~chm/vchembook/553phosglycerides.html [Accessed 10 May. 2014].

J.E. Vance, Dennis E. Vance (2008).&nbsp.Biochemistry of Lipids, Lipoproteins and Membranes. New York: Elsevier. 624.

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Unit Title: Biochemistry

LO5 (Nucleic Acids), Criteria 5.1 to 5.5

To achieve level 3, answer all questions correctly

.

Level 3 (Assessment Criterion 5.1)

Q1There are structural similarities and differences between the nucleic acids RNA and DNA.

a) Describe three structural similarities between RNA and DNA

Presence of a phosphate backbone in both RNA and DNA

Both DNA and RNA contain pentose sugars.

DNA and RNA have 3 nitrogenous bases: Cytosine, Guanine and Adenine

[Q1 continued]

b) Describe two important differences in the molecular structure of RNA and DNA.

The RNA molecule contains Uracil while the DNA contains Thymine

RNA is single stranded while DNA is double stranded

The RNA specific pentose sugar is ribose while DNA specific pentose sugar is deoxyribose.

c) Draw a ribonucleoside

(Clementi, 2010)

and a deoxyribonucleotide.

(state, 2012)Level 3 (Assessment Criterion 5.2)

Q2The Meselsohn / Stahl experiment provided important evidence regarding the mechanism of DNA replication.

a) Briefly describe the experiment and the result.

The experiment was done to prove that DNA replication is semi-conservative in nature. The experiment was based on E.coli DNA. To mark the DNA, the bacteria were grown in a medium containing the heavy N15 isotope of nitrogen. This incorporated the nitrogen in the DNA during the bacterial growth. The DNA was then centrifuged out and transferred to a medium with the N14 isotope and allowed to divide (conditions made suitable). Afterward, the DNA was separated out and both compared to pure 14N and 15N DNA. It was found to have intermediate density, and this thus excluded the conservative theory (Daniel L. Hartl, 2011). This then left the dispersive and semiconservative theories. Further comparisons of densities were used to determine that the DNA formed had two different densities. This thus proved that the semiconservative theory was true. (Daniel L. Hartl, 2011)

b) Outline the model of DNA replication supported by this result.

Semiconservative theory- It states that DNA replication occurs on both DNA strands as they unwind. That is, each single strand of DNA in the pair binds with new bases to form a hybrid of itself and the new bases. The result is a hybrid DNA.

In the diagram, the DNA to the left is the parent DNA. It unwinds and undergoes replication giving the two daughter molecules on the right. But, as is seen, the original parent DNA donates a strand to each daughter molecule thus having an original plus new strand hybrid corresponding to the stipulation of the theory. (biology, 2012)Level 3 (Assessment Criterion 5.3)

Q 3 RNA has numerous important roles in a cell.

a) Which are the three types of RNA involved in protein synthesis?

mRNA – Responsible for carrying the genetic code for the protein out of the nucleus into the cytoplasm for translation.

rRNA – This is the main component of the ribosomes. It is important as the ribosome is the assembly mechanism that leads to the formation/ facilitates polymerisation of the amino acid chains.

tRNA – Responsible for assembly of the individual amino acids as described by the base template of mRNA. It is the amino acid carrier.

b) Compare and contrast the structure and function of mRNA and tRNA molecules.

Similarities. mRNA is responsible for carrying the genetic code out of the nucleus for translation. The tRNA is responsible for attaching and carrying amino acids to facilitate assembly of the growing chain.

They are both RNA in nature and thus possess similar molecular components.

Differences. Structurally, the mRNA and tRNA vary. The mRNA is linear while the tRNA has a conformation similar clover with free ends at the top for the binding functionality.

The mRNA also has more nucleotides than the tRNA.

The tRNA is also possesses a non coding genome, unlike the mRNA

tRNA is found in the cytoplasm while the mRNA is found both in the nucleus and the cytoplasm.

Level 3 (Assessment Criterion 5.4)

Q 4 Transcription and translation are both crucial for the expression of protein-coding genes.

a) Explain how transcription works.

Transcription is the process by which the genetic code for a certain protein (s) is copied unto an mRNA for later translation into a protein. The steps are as follows:

1. Sigma factors initiate the process and facilitate the binding of RNA polymerase to promoter DNA.

2. The RNA polymerase then binds unto the DNA and begins to unzip it forming a transcription bubble. This forms two strands of naked DNA.

3. As the RNA polymerase moves along the strand, it facilitates the joining of nucleotides to complementary bases on the DNA strands.

4. RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand.

5. The Hydrogen bonds of the formed and RNA on the DNA helix break, allowing the RNA strand to detach

6. In nucleated cells, the RNA is further processed with the addition of a 3UTR poly-A tail and a 5UTR cap. It then exits to the cytoplasm through the nuclear pores (Mary Campbell, 2011) (Passarge, 2011), to be bound to ribosomes for translation.

b) Explain how translation works.

Translation is the process by which the mRNA is converted to polypeptide chains in the cytoplasm.

mRNA is carried into the cytoplasm trough the nuclear pore. Here, it binds to the ribosomal complex. The tRNA then follows up with the portions of amino acids required for the polypeptide chain to be assembled. Subsequent tRNAs follow up with amino acids and bind while leaving space for the next complex. Aminoacyl tRNA transferase is responsible for catalyzing the bond between tRNAs and their specific amino acids. The synthesized chain is then secreted into the endoplasmic reticulum (Passarge, 2011) and prepared for post translational modification.Level 3 (Assessment Criterion 5.5)

Q 5All organisms on this planet use the same genetic code.

a) How does one look up a codon in the ‘codon sun’ diagram, and which TWO key features of the code does it illustrate? To look up a codon, one has to first know that 3 bases comprise a codon. The centre base is the first. The second is in the center circle, while the third id in the outermost. Therefore for one to look up a codon, one reads in going out. The main aspecs highlighted are that one, Thymine is replaced by uracil. Two, several codons may code a single amino acid.

b) Which polypeptides would be produced from translation of the synthetic RNAs poly (A), poly(C), poly(G) and poly(U), respectively?

Poly A- Lysine, (K) a basic amino acid formed from the expression of the AAA codon.

Poly C- Proline, (P) an aromatic amino acid formed from the expression of the CCC codon.

Poly G- Glycine,(G) an amino acid formed from the expression of the GGG codon. It is the smallest amino acid with a hydrogen molecule as its side chain.

Poly U- Phenylalanine, (F) an amino acid formed from the expression of the UUU codon. It is aromatic and known to be electrically neutral.

Lys-pro-glyc-phe

Bibliography 3 (ribonucleotides)

Clementi, N., Chirkova, A., Puffer, B., Micura, R. and Polacek, N. (2010). Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation.&nbsp.Nature Chemical Biology, [online] 6(5), p.344. Available at: http://www.nature.com/nchembio/journal/v6/n5/compound/nchembio.341_ci.html [Accessed 10 May. 2014].

Daniel L. Hartl, Maryellen Ruvolo (2011).&nbsp.Genetics. New York: Jones & Bartlett Publishers. 860.

Eberhard Passarge (2012).&nbsp.Color atlas of genetics. 4th ed. New York: Thieme. 496

Kennesaw state university. (2014).&nbsp.Deoxyribonucleotide.&nbsp.Available: http://chemcases.com/cisplat/cisplat14.htm. Last accessed 04/05/2014.

Mary Campbell, Shawn Farrell (2014).&nbsp.Biochemistry.. New York: Cengage learning. 864.

Pass biology. (2013).&nbsp.Cells.&nbsp.Available: http://www.passbiology.co.nz/biology-level-2/cells. Last accessed 04/05/2014.